First of all I want to propose that there be no fixed limit on the GPs. GPs should be volatile, and the way to be a GP would be to actually take part in a war (doesn't have to be leading) and have a mayor contribution to the war. War contribution is handled in CK2 and EUIV so I don't know why it wouldn't be in V3.
I also want to propose the addition of a LOT more of resources. No "dumbing" it down, it's way to arbitrary at times and fails to represent most of the world's nations' produce. For example, Argentina back in 1880-1930 had an agroexportation model which basically meant that we exported mostly stuff RELATED to livestock. That means take a cow, kill it and sell its produce. What does it produce? A lot. You can produce milk with the cow alive, you can make meat and leather. That's 3 products that are easily used for different things IRL. Milk perishes quickly, while meat would behave that way before refrigerators (salt was used before them).
I support the notion of "continental" SOIs but you should keep in mind nations in South America where there is a serious problem of "trade" by land. For example, Chile wouldn't normally trade with Argentina by land (Andes?) And Paraguay is effed if they don't have an exit to a river (better representation of rivers is a must as well.) as they are in a pretty bad spot, so is Bolivia if they lose the access to the sea. I would love to have infrastructure deal a serious impact on the pops.
People living in the middle of the amazonas would not have the access to goods that someone living in Rio would. Mainly because people in Rio live next to the sea, making goods easier to come by. That is a reality today and should be even more impacting before.
I speak for my country, but a better representation of the entire "divisions" of the map could be created. First of all, states are a good... start, but a very lazy one. States should be created at the game start by default but they should be changeable. A lot of states in Germany were actually nations before, so that should be kept as a model later on. If Bavaria blobs a bit before Germany is formed, the state of Bavaria should remain kind of independent, kind of like vassals in CK2. Depending on the constitution of the nation or "crown laws" however you want to call it. (Constitutions might be a good idea. Simplify it to a political paradigm. Say a conservative constitution will allow far less changes than a socialist one for example). States could be created from other states to weaken "vassals".
In the new world, you could also have a nice system where you create your own states. You can have a BIG state all around the west coast of the united states, but such a huge vassal would be bad, right? so you make a lot smaller ones, but that's just as bad as they have no economical autonomy.
A fine balance should be set in the middle. And of course, Governors should be implemented. If a "province" or "state" votes radical it should affect that state and of course the upperhouse. Argentina actually had a constitution that allowed for the president to "intervene" a province and call for new elections if they didn't like the outcome. (conservative constitution anyone?)
Regarding the actual content of those "states" it should be a bit different than the actual model. I want to propose something similar to CK2 where you have a "capital" and several other settlements. The capital should be the district capital and will of course be a city. The other 3 settlements should all be towns. You won't have the chance to build "forts" or "farms", only new towns. BEHIND the capital and the 3 settlements there should be a "generalized" farmland that produces whatever farm-ish goods you can imagine. Of course, if you're in a mountain, you'll have a mountain. Farmland should produce around 3 or 4 products. Say your farlmand produces "livestock" which it then sells to the city/towns which process it and either consume it or sell it around. The city then could sell it to other cities or towns from the other actual provinces clausewitz divides the game map in. However if there is no demand for the good, the pops in those cities or towns will either stock it or export it.
Most of the time they'll sell it to a bunch of aristocrats or Capitalists in the big cities next to ports which then sell it to the foreign markets. Which is when infrastructure comes in. without proper railways, those provinces in the background of your nation are effectively cut off. Farm goods cannot be sold outside of that market, and only manufactured goods can be brought in by horse or stuff but it's pretty damn sure that you won't have anything interesting coming out of that province. It's the way a lot of people lived in the americas outside of the big places. They created an autonomous economy if they were not within reach of the railways.
I also want to propose a total reshaping of the research section. Research should not be decided by the government, rather by the pops. Exception is communism, but it should be very inneficient. Maybe a new use for Capitalism is to actually own a corporation. That corporation employs pops. In a country like Argentina which exports a lot of goods, their corporation would most likely be a trade oriented corp, so it's not going to be researching stuff outside of trade oriented stuff like railways and factories.
Clergymen and universitaries (new pop?) could be studying the "prestige" branch of research.
Soldiers and Officers work on the "military" aspect. However, there is no clear research path. It proceeds on it's own. High Literacy helps a lot, as well as having a lot of infrastructure between your big pop sites (more stories do reach the capital than they do reach Vladivostok).
Hmm... what else.
Of course, different currencies. I'm not telling PDS to work on every currency of every country, I'm asking them to set a "gold price" for a product that the market defines, and then every nation has it's "currency" affected by a porcentual value representing it's standard. For example, using a silver standard means that you have "more" money but less money in absolute values. This would affect the pops at the time of importing and exporting.
Anywho, I'm out of steam to write at the moment. I do have more ideas I'll post later.
Cheers